Drosophila melanogaster genome annotation release 4.1.1 date 20050421 DATA CONTENTS Feature counts in release 4, 3 compared annotation features (r40 nov04, r322 oct 04, r320 March 04) Table of D. mel. genome feature counts per release. Feature 411 410 400 322 ------------------------------------------------------------ BAC 706 674 0 949 CDS 18941 18941 18715 18747 DNA_motif 5 5 5 5 RNA_motif 0 0 0 1 aberration_junction 86 86 86 86 chromosome_arm 6 6 6 6 chromosome_band 5770 5770 0 5715 enhancer 27 27 27 27 five_prime_UTR 14641 14641 14360 15769 gene 13449 13449 13472 13472 insertion_site 457 457 457 457 intron 16362 16362 16135 16153 mRNA 19572 19572 19301 19302 mRNA_genscan 0 0 0 19189 mRNA_piecegenie 0 0 0 13794 match_HDP 139 139 139 2448 match_RNAiHDP 110 110 110 40 match_assembly_path 434 434 434 0 match_blastx_aa_SP.hyp.dros 0 0 0 354 match_blastx_aa_SP.real.dros 0 0 0 22163 match_blastx_aa_SPTR.dmel 207911 207911 207911 0 match_blastx_aa_SPTR.dros 0 0 0 68846 match_blastx_aa_SPTR.insect 16610 16610 16610 7492 match_blastx_aa_SPTR.othinv 21451 21451 21451 12471 match_blastx_aa_SPTR.othvert 18036 18036 18036 11774 match_blastx_aa_SPTR.plant 11997 11997 11997 9609 match_blastx_aa_SPTR.primate 20850 20850 20850 16345 match_blastx_aa_SPTR.rodent 21644 21644 21644 16081 match_blastx_aa_SPTR.worm 13765 13765 13765 12679 match_blastx_aa_SPTR.yeast 5593 5593 5593 5211 match_blastx_aa_TR.real.dros 0 0 0 43823 match_blastx_aa_users_i.dros 0 0 0 4633 match_fgenesh 0 0 0 14837 match_genie 11063 11063 11063 0 match_genscan 17811 17811 17811 0 match_repeat_runner_seg 0 0 9198 0 match_repeatmasker 11758 11758 11758 0 match_sim4_na_ARGs.dros 1062 1062 1062 0 match_sim4_na_ARGsCDS.dros 984 984 984 0 match_sim4_na_DGC.dros 0 0 0 15270 match_sim4_na_DGC_dros 6458 6458 5159 0 match_sim4_na_EST.all_nr.dros 0 0 0 267828 match_sim4_na_adh.cDNAs.dros 0 0 0 51 match_sim4_na_cDNA.dros 0 0 0 10319 match_sim4_na_dbEST.diff.dmel 85910 85910 82910 0 match_sim4_na_dbEST.same.dmel 169078 169078 159793 0 match_sim4_na_gadfly.dros.RE.. 0 0 0 14389 match_sim4_na_gadfly_dmel_r2 14249 14249 14249 0 match_sim4_na_gb.dmel 26531 26531 26531 0 match_sim4_na_gb.dros 0 0 0 14977 match_sim4_na_gb.tpa.dmel 2214 2214 2214 0 match_sim4_na_pe.dros 0 0 0 3201 match_sim4_na_smallRNA.dros 98 98 98 0 match_sim4_na_transcript_dme.. 19001 19001 19001 0 match_sim4_na_transcript_dme.. 18799 18799 18799 0 match_sim4tandem_na_gb.dmel 28787 23748 23748 0 match_tRNAscan-SE 295 295 295 0 match_tblastx_na_agambiae 101190 101190 101190 0 match_tblastx_na_dbEST.insect 34107 34107 34107 16818 match_tblastx_na_dpse 263465 263465 263465 0 match_tblastx_na_unigene.rod.. 0 0 0 11707 mature_peptide 7 7 7 7 ncRNA 130 130 70 70 oligo 197525 197525 0 197726 orthologous_region 0 0 0 12101 point_mutation 485 485 485 485 polyA_site 107 107 107 107 protein_binding_site 90 90 90 90 pseudogene 39 39 40 40 rRNA 96 96 96 96 region 30 30 30 30 regulatory_region 137 137 137 137 repeat_region 9199 9199 1 4652 rescue_fragment 136 136 136 136 scaffold 437 437 437 437 sequence_variant 232 232 232 232 snRNA 29 29 28 28 snoRNA 28 28 28 28 source 6 6 6 6 syntenic_region 0 0 0 1230 tRNA 295 295 288 288 tRNA_trnascan 0 0 0 297 three_prime_UTR 15018 15019 14683 16777 transcription_start_site 36921 36921 36921 35737 transposable_element 1571 1571 1571 1572 transposable_element_inserti.. 16404 16404 4680 3257 transposable_element_pred 0 0 0 1572 ------------------------------------------------------------ -- == data not available for this feature Category clarification: gene = protein coding gene, other features with gene-models (and transcripts) are pseudogene, rRNA, snRNA, snoRNA, tRNA, ncRNA mRNA = all transcript types including from pseudogene, rRNA, snRNA, snoRNA, tRNA, ncRNA ------- Data are from Postgres Chado database, release 4.1.1, 21 apr 2005 BULK FILE SET See ftp://flybase.net/genomes/Drosophila_melanogaster/dmel_r4.1.1_20050421/ blast/ - NCBI blast database set for selected fasta/ feature sets. dna/ - contains dna raw format files per chromosome-arm fasta/ - dna and protein data per chromosome and feature type; and -all- files which catenate each chromosome set. chromosome dna in fasta format gff/ - GFF v3 standard feature files per chromosome gnomap/ - Gnomap standard feature files per chromosome (drive genome map views) These two contain chromosome locations of above listed features pgsql/ - PostgreSQL Chado database dump files tables/ - Tabular lists of feature counts, IDs, and related summary information xml-chado/ - Chado XML output of database xml-game/ - GAME XML output of database